Table 5: Mapping statistics for three threat agents and our Bgcalibrant. Nonalignment
Z values are included for comparison. The higher Z values for
Bukholderia is reflective of the higher fraction of non-reference-matching base calls
in these samples and is indicative of a greater population diversity compared to Bg.
Bukholderia had much higher SNP calls (Pipeline B) compared to the Y. pestis. The
larger unmapped base counts along the reference genomes (column 5) for Yp and
Bm are due to insertion elements that are highly mobile within these genomes and
promote re-arrangements. The BFAST default parameters for assigning candidate
locations to reads when there is a high multiplicity of candidate alignments across
the reference genome resulted in these gaps.